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This is waiting for us to define the "language" of edam classifiers that we are going to support. Currently we only define services by what operation they perform but there is plenty of room for fi...

This is waiting for us to define the "language" of edam classifiers that we are going to support. Currently we only define services by what operation they perform but there is plenty of room for fine grained tuning of operations based on other classifiers.

Yes, there are pieces of code that can be reused across multiple if not all other workers. I suppose we can either add component classes that can be used by the workers that need them or we can cre...

Yes, there are pieces of code that can be reused across multiple if not all other workers. I suppose we can either add component classes that can be used by the workers that need them or we can create an abstract base class for all workers with implementations of common methods. The purpose of operation class is to provide metadata and create a worker, so the operation should stay as it is, but the worker needs to be tidied up. I absolutely agree that currently it is too bloated and should be split into smaller pieces but for now I wanted something that just works.
Regarding tuning, the whole point is that now the service is made of operations instead of extending one, so we can create new operations or add extra parameters to the existing operation classes that would alter worker behaviour without touching other parts of the code.

after taking a look at the rest I can see that the next step is to split this class up further. There's plenty of code that will be used by many different operations - e.g. job state management - i...

after taking a look at the rest I can see that the next step is to split this class up further. There's plenty of code that will be used by many different operations - e.g. job state management - is that the plan ?

not really the recommended way - see e.g. https://docs.oracle.com/en/java/javase/11/docs/api/java.desktop/java/beans/PropertyChangeSupport.html *do you need to expose the generic binders ? what k...

not really the recommended way - see e.g. https://docs.oracle.com/en/java/javase/11/docs/api/java.desktop/java/beans/PropertyChangeSupport.html

  • do you need to expose the generic binders ? what kind of events need to be monitored ?
is utils really the right name ? suggest the classes are used in several different places

is utils really the right name ? suggest the classes are used in several different places

this is going to get much more complex. there are plenty of additional attributes - e.g. input type (dna, protein, rna) - none of them are currently being configured on the operation.

this is going to get much more complex. there are plenty of additional attributes - e.g. input type (dna, protein, rna) - none of them are currently being configured on the operation.

this class seems to contain a bunch of hard coded stuff taken from the original web services configuration code rather than provide a way for a web services provider to configure an instance of Ali...

this class seems to contain a bunch of hard coded stuff taken from the original web services configuration code rather than provide a way for a web services provider to configure an instance of AlignmentOperation tuned to the alignment service that the provider is offering.

first review of Web Services overhaul for 2.12
first review of Web Services overhaul for 2.12
JAL-3878 Remove throws declaration from param store construction.

Add RNAalifold service instance to slivka web services.

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    ./RNAalifoldServiceInstance.java
Merge branch 'improvement/JAL-3848_slivka_0.8' into alpha/JAL-3066_Jalview_212_slivka-integration

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Merge branch 'bug/JAL-3807_jpred-with-slivka' into alpha/JAL-3066_Jalview_212_slivka-integration

JAL-3848 ensure annotation from a service gets a calcId so it can be updated and tracked across multiple views - nb - service.getId() probably isn’t the right value to use for this!

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    ./SlivkaAnnotationServiceInstance.java
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JAL-3848 don’t include sequence limits in sequence id as it confuses slivka-0.8’s jalview-feature-file creation script

Merge branch 'jpred-fix' into bug/JAL-3807_jpred-with-slivka

JAL-3807 Fix SlivkaWSInstance not fetching alignments.

JAL-3848 SlivkaParamSet: reformat code and add service description.

WIP
WIP
JAL-3848 Update slivka client library.

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    ./SlivkaAnnotationServiceInstance.java
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WIP

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    ./SlivkaAnnotationServiceInstance.java
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Revert "Merge branch 'bug/JAL-3807_jpred-with-slivka' into alpha/JAL-3066_Jalview_212_slivka-integration"

This reverts commit 95f4ae66fbaecbbdc1c3ab3c6c9c611a3a9a3e46, reversing

changes made to bc7c2cf5500c5a4124a69ef8e7b1374d8997558f.

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Merge branch 'bug/JAL-3807_jpred-with-slivka' into alpha/JAL-3066_Jalview_212_slivka-integration

JAL-3807 - Add single sequence capabilities to jws2.JPredClient

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JAL-3807 - Add single sequence capabilities to jws2.JPredClient

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JAL-3807 - Re-implement results processing.

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JAL-3807 - Re-implement results processing.

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This one should be compiling

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